A Next-Generation Marker Genotyping Platform (AmpSeq) in Heterozygous Crops: A Case Study for Marker Assisted Selection in Grapevine

Marker assisted selection (MAS) has become widely used in perennial crop breeding programs to accelerate and enhance cultivar development via selection during the juvenile phase and parental selection prior to crossing. Next generation sequencing (NGS) has been widely used for whole genome molecular marker discovery, but it also offers a potential opportunity for tailored molecular marker development with high-throughput and low per-sample cost. This study presents a novel and efficient MAS strategy for molecular marker development incorporating a semi-automated primer design pipeline based on amplicon sequencing (AmpSeq). The results document the development of an MAS package using three relevant traits (flower sex, disease resistance, and modified anthocyanins) in grapevine breeding. Here we discuss several strengths of the amplicon sequencing platform that make this approach of broad interest in diverse crop species: accuracy, flexibility, high throughput, low cost, easily automated analysis, and rapid results.